It seems like on most stack exhcnage website the reputation for the meta and the main site is the same. Was wondering if there is any reason why it's seperated on SO. It makes sense for someone who is active enough in SO to have some say in meta.

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meta Stack Overflow isn't really meta Stack Overflow, it's meta Stack Exchange, the meta for the entire Stack Exchange network (in addition to being the only meta for Stack overflow), so it doesn't make sense to stifle users from other Stack Exchange sites by merging its rep with SO's rep.